I made my changes using IDA but I don't know how to make the new file exe again
A:
According to a discussion on OpenRCE, it seems that you cannot directly force IDA Pro to output an ".exe". What you can do is get it to produce a ".dif" and use that to patch the original ".exe".
To get IDA Pro to generate the ".dif": File->Produce file->Create
John Mulder
2009-01-31 02:35:27